public bool XMLOutputFileInitialize(
string inputFilePathFull,
string outputDirectoryPath,
clsDataOutput dataOutputHandler,
clsScanList scanList,
clsSpectraCache spectraCache,
clsSICOptions sicOptions,
clsBinningOptions binningOptions)
{
var xmlOutputFilePath = string.Empty;
try
{
xmlOutputFilePath = clsDataOutput.ConstructOutputFilePath(inputFilePathFull, outputDirectoryPath, clsDataOutput.eOutputFileTypeConstants.XMLFile);
dataOutputHandler.OutputFileHandles.XMLFileForSICs = new XmlTextWriter(xmlOutputFilePath, System.Text.Encoding.UTF8);
var writer = dataOutputHandler.OutputFileHandles.XMLFileForSICs;
writer.Formatting = Formatting.Indented;
writer.Indentation = 1;
writer.WriteStartDocument(true);
writer.WriteStartElement("SICData");
writer.WriteStartElement("ProcessingSummary");
writer.WriteElementString("DatasetID", sicOptions.DatasetID.ToString());
writer.WriteElementString("SourceFilePath", inputFilePathFull);
string lastModTimeText;
string fileSizeBytes;
try
{
var inputFileInfo = new FileInfo(inputFilePathFull);
var lastModTime = inputFileInfo.LastWriteTime;
lastModTimeText = lastModTime.ToShortDateString() + " " + lastModTime.ToShortTimeString();
fileSizeBytes = inputFileInfo.Length.ToString();
}
catch (Exception ex)
{
lastModTimeText = string.Empty;
fileSizeBytes = "0";
}
writer.WriteElementString("SourceFileDateTime", lastModTimeText);
writer.WriteElementString("SourceFileSizeBytes", fileSizeBytes);
writer.WriteElementString("MASICProcessingDate", DateTime.Now.ToString(clsDatasetStatsSummarizer.DATE_TIME_FORMAT_STRING));
writer.WriteElementString("MASICVersion", mOptions.MASICVersion);
writer.WriteElementString("MASICPeakFinderDllVersion", mOptions.PeakFinderVersion);
writer.WriteElementString("ScanCountTotal", scanList.MasterScanOrderCount.ToString());
writer.WriteElementString("SurveyScanCount", scanList.SurveyScans.Count.ToString());
writer.WriteElementString("FragScanCount", scanList.FragScans.Count.ToString());
writer.WriteElementString("SkipMSMSProcessing", mOptions.SkipMSMSProcessing.ToString());
writer.WriteElementString("ParentIonDecoyMassDa", mOptions.ParentIonDecoyMassDa.ToString("0.0000"));
writer.WriteEndElement();
writer.WriteStartElement("MemoryOptions");
writer.WriteElementString("CacheAlwaysDisabled", spectraCache.DiskCachingAlwaysDisabled.ToString());
writer.WriteElementString("CacheSpectraToRetainInMemory", spectraCache.CacheSpectraToRetainInMemory.ToString());
writer.WriteEndElement();
writer.WriteStartElement("SICOptions");
// SIC Options
// "SICToleranceDa" is a legacy parameter; If the SIC tolerance is in PPM, then "SICToleranceDa" is the Da tolerance at 1000 m/z
writer.WriteElementString("SICToleranceDa", clsParentIonProcessing.GetParentIonToleranceDa(sicOptions, 1000).ToString("0.0000"));
writer.WriteElementString("SICTolerance", sicOptions.SICTolerance.ToString("0.0000"));
writer.WriteElementString("SICToleranceIsPPM", sicOptions.SICToleranceIsPPM.ToString());
writer.WriteElementString("RefineReportedParentIonMZ", sicOptions.RefineReportedParentIonMZ.ToString());
writer.WriteElementString("ScanRangeStart", sicOptions.ScanRangeStart.ToString());
writer.WriteElementString("ScanRangeEnd", sicOptions.ScanRangeEnd.ToString());
writer.WriteElementString("RTRangeStart", sicOptions.RTRangeStart.ToString(CultureInfo.InvariantCulture));
writer.WriteElementString("RTRangeEnd", sicOptions.RTRangeEnd.ToString(CultureInfo.InvariantCulture));
writer.WriteElementString("CompressMSSpectraData", sicOptions.CompressMSSpectraData.ToString());
writer.WriteElementString("CompressMSMSSpectraData", sicOptions.CompressMSMSSpectraData.ToString());
writer.WriteElementString("CompressToleranceDivisorForDa", sicOptions.CompressToleranceDivisorForDa.ToString("0.0"));
writer.WriteElementString("CompressToleranceDivisorForPPM", sicOptions.CompressToleranceDivisorForPPM.ToString("0.0"));
writer.WriteElementString("MaxSICPeakWidthMinutesBackward", sicOptions.MaxSICPeakWidthMinutesBackward.ToString(CultureInfo.InvariantCulture));
writer.WriteElementString("MaxSICPeakWidthMinutesForward", sicOptions.MaxSICPeakWidthMinutesForward.ToString(CultureInfo.InvariantCulture));
writer.WriteElementString("IntensityThresholdFractionMax", StringUtilities.DblToString(sicOptions.SICPeakFinderOptions.IntensityThresholdFractionMax, 5));
writer.WriteElementString("IntensityThresholdAbsoluteMinimum", sicOptions.SICPeakFinderOptions.IntensityThresholdAbsoluteMinimum.ToString(CultureInfo.InvariantCulture));
// Peak Finding Options
var baselineNoiseOptions = sicOptions.SICPeakFinderOptions.SICBaselineNoiseOptions;
writer.WriteElementString("SICNoiseThresholdMode", baselineNoiseOptions.BaselineNoiseMode.ToString());
writer.WriteElementString("SICNoiseThresholdIntensity", baselineNoiseOptions.BaselineNoiseLevelAbsolute.ToString(CultureInfo.InvariantCulture));
writer.WriteElementString("SICNoiseFractionLowIntensityDataToAverage", StringUtilities.DblToString(baselineNoiseOptions.TrimmedMeanFractionLowIntensityDataToAverage, 5));
writer.WriteElementString("SICNoiseMinimumSignalToNoiseRatio", baselineNoiseOptions.MinimumSignalToNoiseRatio.ToString(CultureInfo.InvariantCulture));
writer.WriteElementString("MaxDistanceScansNoOverlap", sicOptions.SICPeakFinderOptions.MaxDistanceScansNoOverlap.ToString());
writer.WriteElementString("MaxAllowedUpwardSpikeFractionMax", StringUtilities.DblToString(sicOptions.SICPeakFinderOptions.MaxAllowedUpwardSpikeFractionMax, 5));
writer.WriteElementString("InitialPeakWidthScansScaler", sicOptions.SICPeakFinderOptions.InitialPeakWidthScansScaler.ToString(CultureInfo.InvariantCulture));
writer.WriteElementString("InitialPeakWidthScansMaximum", sicOptions.SICPeakFinderOptions.InitialPeakWidthScansMaximum.ToString());
writer.WriteElementString("FindPeaksOnSmoothedData", sicOptions.SICPeakFinderOptions.FindPeaksOnSmoothedData.ToString());
writer.WriteElementString("SmoothDataRegardlessOfMinimumPeakWidth", sicOptions.SICPeakFinderOptions.SmoothDataRegardlessOfMinimumPeakWidth.ToString());
writer.WriteElementString("UseButterworthSmooth", sicOptions.SICPeakFinderOptions.UseButterworthSmooth.ToString());
writer.WriteElementString("ButterworthSamplingFrequency", StringUtilities.DblToString(sicOptions.SICPeakFinderOptions.ButterworthSamplingFrequency, 5));
writer.WriteElementString("ButterworthSamplingFrequencyDoubledForSIMData", sicOptions.SICPeakFinderOptions.ButterworthSamplingFrequencyDoubledForSIMData.ToString());
writer.WriteElementString("UseSavitzkyGolaySmooth", sicOptions.SICPeakFinderOptions.UseSavitzkyGolaySmooth.ToString());
writer.WriteElementString("SavitzkyGolayFilterOrder", sicOptions.SICPeakFinderOptions.SavitzkyGolayFilterOrder.ToString());
var noiseThresholdOptions = sicOptions.SICPeakFinderOptions.MassSpectraNoiseThresholdOptions;
writer.WriteElementString("MassSpectraNoiseThresholdMode", noiseThresholdOptions.BaselineNoiseMode.ToString());
writer.WriteElementString("MassSpectraNoiseThresholdIntensity", noiseThresholdOptions.BaselineNoiseLevelAbsolute.ToString(CultureInfo.InvariantCulture));
writer.WriteElementString("MassSpectraNoiseFractionLowIntensityDataToAverage", StringUtilities.DblToString(noiseThresholdOptions.TrimmedMeanFractionLowIntensityDataToAverage, 5));
writer.WriteElementString("MassSpectraNoiseMinimumSignalToNoiseRatio", noiseThresholdOptions.MinimumSignalToNoiseRatio.ToString(CultureInfo.InvariantCulture));
writer.WriteElementString("ReplaceSICZeroesWithMinimumPositiveValueFromMSData", sicOptions.ReplaceSICZeroesWithMinimumPositiveValueFromMSData.ToString());
writer.WriteElementString("SaveSmoothedData", sicOptions.SaveSmoothedData.ToString());
// Similarity options
writer.WriteElementString("SimilarIonMZToleranceHalfWidth", sicOptions.SimilarIonMZToleranceHalfWidth.ToString(CultureInfo.InvariantCulture));
writer.WriteElementString("SimilarIonToleranceHalfWidthMinutes", sicOptions.SimilarIonToleranceHalfWidthMinutes.ToString(CultureInfo.InvariantCulture));
writer.WriteElementString("SpectrumSimilarityMinimum", sicOptions.SpectrumSimilarityMinimum.ToString(CultureInfo.InvariantCulture));
writer.WriteEndElement();
writer.WriteStartElement("BinningOptions");
writer.WriteElementString("BinStartX", binningOptions.StartX.ToString(CultureInfo.InvariantCulture));
writer.WriteElementString("BinEndX", binningOptions.EndX.ToString(CultureInfo.InvariantCulture));
writer.WriteElementString("BinSize", binningOptions.BinSize.ToString(CultureInfo.InvariantCulture));
writer.WriteElementString("MaximumBinCount", binningOptions.MaximumBinCount.ToString());
writer.WriteElementString("IntensityPrecisionPercent", binningOptions.IntensityPrecisionPercent.ToString(CultureInfo.InvariantCulture));
writer.WriteElementString("Normalize", binningOptions.Normalize.ToString());
writer.WriteElementString("SumAllIntensitiesForBin", binningOptions.SumAllIntensitiesForBin.ToString());
writer.WriteEndElement();
writer.WriteStartElement("CustomSICValues");
writer.WriteElementString("MZList", mOptions.CustomSICList.RawTextMZList);
writer.WriteElementString("MZToleranceDaList", CheckForEmptyToleranceList(mOptions.CustomSICList.RawTextMZToleranceDaList));
writer.WriteElementString("ScanCenterList", mOptions.CustomSICList.RawTextScanOrAcqTimeCenterList);
writer.WriteElementString("ScanToleranceList", CheckForEmptyToleranceList(mOptions.CustomSICList.RawTextScanOrAcqTimeToleranceList));
writer.WriteElementString("ScanTolerance", mOptions.CustomSICList.ScanOrAcqTimeTolerance.ToString(CultureInfo.InvariantCulture));
writer.WriteElementString("ScanType", mOptions.CustomSICList.ScanToleranceType.ToString());
writer.WriteElementString("LimitSearchToCustomMZList", mOptions.CustomSICList.LimitSearchToCustomMZList.ToString());
writer.WriteEndElement();
}
catch (Exception ex)
{
ReportError("Error initializing the XML output file: " + xmlOutputFilePath, ex, clsMASIC.eMasicErrorCodes.OutputFileWriteError);
return(false);
}
return(true);
}
private bool ExtractXcaliburFragmentationScan(
XRawFileIO xcaliburAccessor,
clsScanList scanList,
clsSpectraCache spectraCache,
clsDataOutput dataOutputHandler,
clsSICOptions sicOptions,
clsBinningOptions binningOptions,
ThermoRawFileReader.clsScanInfo thermoScanInfo)
{
// Note that MinimumPositiveIntensity will be determined in LoadSpectraForThermoRawFile
var scanInfo = new clsScanInfo(thermoScanInfo.ParentIonMZ)
{
ScanNumber = thermoScanInfo.ScanNumber,
ScanTime = (float)thermoScanInfo.RetentionTime,
ScanHeaderText = XRawFileIO.MakeGenericThermoScanFilter(thermoScanInfo.FilterText),
ScanTypeName = XRawFileIO.GetScanTypeNameFromThermoScanFilterText(thermoScanInfo.FilterText),
BasePeakIonMZ = thermoScanInfo.BasePeakMZ,
BasePeakIonIntensity = thermoScanInfo.BasePeakIntensity,
TotalIonIntensity = thermoScanInfo.TotalIonCurrent,
MinimumPositiveIntensity = 0,
ZoomScan = thermoScanInfo.ZoomScan,
SIMScan = thermoScanInfo.SIMScan,
MRMScanType = thermoScanInfo.MRMScanType
};
// Typically .EventNumber is 1 for the parent-ion scan; 2 for 1st frag scan, 3 for 2nd frag scan, etc.
// This resets for each new parent-ion scan
scanInfo.FragScanInfo.FragScanNumber = thermoScanInfo.EventNumber - 1;
// The .EventNumber value is sometimes wrong; need to check for this
// For example, if the dataset only has MS2 scans and no parent-ion scan, .EventNumber will be 2 for every MS2 scan
if (scanList.FragScans.Count > 0)
{
var prevFragScan = scanList.FragScans[scanList.FragScans.Count - 1];
if (prevFragScan.ScanNumber == scanInfo.ScanNumber - 1)
{
if (scanInfo.FragScanInfo.FragScanNumber <= prevFragScan.FragScanInfo.FragScanNumber)
{
scanInfo.FragScanInfo.FragScanNumber = prevFragScan.FragScanInfo.FragScanNumber + 1;
}
}
}
scanInfo.FragScanInfo.MSLevel = thermoScanInfo.MSLevel;
if (scanInfo.MRMScanType != MRMScanTypeConstants.NotMRM)
{
// This is an MRM scan
scanList.MRMDataPresent = true;
scanInfo.MRMScanInfo = clsMRMProcessing.DuplicateMRMInfo(thermoScanInfo.MRMInfo, thermoScanInfo.ParentIonMZ);
if (scanList.SurveyScans.Count == 0)
{
// Need to add a "fake" survey scan that we can map this parent ion to
mLastNonZoomSurveyScanIndex = scanList.AddFakeSurveyScan();
}
}
else
{
scanInfo.MRMScanInfo.MRMMassCount = 0;
}
scanInfo.LowMass = thermoScanInfo.LowMass;
scanInfo.HighMass = thermoScanInfo.HighMass;
scanInfo.IsFTMS = thermoScanInfo.IsFTMS;
// Store the ScanEvent values in .ExtendedHeaderInfo
StoreExtendedHeaderInfo(dataOutputHandler, scanInfo, thermoScanInfo.ScanEvents);
// Store the collision mode and possibly the scan filter text
scanInfo.FragScanInfo.CollisionMode = thermoScanInfo.CollisionMode;
StoreExtendedHeaderInfo(dataOutputHandler, scanInfo, clsExtendedStatsWriter.EXTENDED_STATS_HEADER_COLLISION_MODE, thermoScanInfo.CollisionMode);
if (mOptions.WriteExtendedStatsIncludeScanFilterText)
{
StoreExtendedHeaderInfo(dataOutputHandler, scanInfo, clsExtendedStatsWriter.EXTENDED_STATS_HEADER_SCAN_FILTER_TEXT, thermoScanInfo.FilterText);
}
if (mOptions.WriteExtendedStatsStatusLog)
{
// Store the StatusLog values in .ExtendedHeaderInfo
StoreExtendedHeaderInfo(dataOutputHandler, scanInfo, thermoScanInfo.StatusLog, mOptions.StatusLogKeyNameFilterList);
}
scanList.FragScans.Add(scanInfo);
var fragScanIndex = scanList.FragScans.Count - 1;
scanList.AddMasterScanEntry(clsScanList.eScanTypeConstants.FragScan, fragScanIndex);
// Note: Even if keepRawSpectra = False, we still need to load the raw data so that we can compute the noise level for the spectrum
var msDataResolution = binningOptions.BinSize / sicOptions.CompressToleranceDivisorForDa;
var success = LoadSpectraForThermoRawFile(
xcaliburAccessor,
spectraCache,
scanInfo,
sicOptions.SICPeakFinderOptions.MassSpectraNoiseThresholdOptions,
clsMASIC.DISCARD_LOW_INTENSITY_MSMS_DATA_ON_LOAD,
sicOptions.CompressMSMSSpectraData,
msDataResolution,
mKeepRawSpectra && mKeepMSMSSpectra);
if (!success)
{
return(false);
}
SaveScanStatEntry(dataOutputHandler.OutputFileHandles.ScanStats, clsScanList.eScanTypeConstants.FragScan, scanInfo, sicOptions.DatasetID);
if (thermoScanInfo.MRMScanType == MRMScanTypeConstants.NotMRM)
{
// This is not an MRM scan
mParentIonProcessor.AddUpdateParentIons(scanList, mLastNonZoomSurveyScanIndex, thermoScanInfo.ParentIonMZ,
fragScanIndex, spectraCache, sicOptions);
}
else
{
// This is an MRM scan
mParentIonProcessor.AddUpdateParentIons(scanList, mLastNonZoomSurveyScanIndex, thermoScanInfo.ParentIonMZ,
scanInfo.MRMScanInfo, spectraCache, sicOptions);
}
if (mLastNonZoomSurveyScanIndex >= 0)
{
var precursorScanNumber = scanList.SurveyScans[mLastNonZoomSurveyScanIndex].ScanNumber;
// Compute the interference of the parent ion in the MS1 spectrum for this frag scan
scanInfo.FragScanInfo.InterferenceScore = ComputeInterference(xcaliburAccessor, thermoScanInfo, precursorScanNumber);
}
return(true);
}